I have looked through the Blizzard settings and it appears my window background no longer changes from black to transparent and then back to black when a mouseover occurs. Is this just the patch or a setting I am missing?

Looks like you'll need to do something similar to the timestamps fix with mouswheel scrolling, as well. If I turn on mousewheel in the chat interface, and its on in Chatter, it's fine. If I turn off the mousewheel scrolling in the interface, but it is on in Chatter, it works intermittently.